forked from lijiext/lammps
download only the plumed-src package and include further tweaks to be compatible with plumed 2.5b
This commit is contained in:
Axel Kohlmeyer
parent
ac11d66d5a
commit
badfdd7433
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@ -15,7 +15,7 @@ kspace_style pppm 0.0001
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read_data data.peptide
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orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
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1 by 1 by 2 MPI processor grid
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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2004 atoms
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reading velocities ...
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@ -85,7 +85,7 @@ PPPM initialization ...
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estimated absolute RMS force accuracy = 0.0228209
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estimated relative force accuracy = 6.87243e-05
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using double precision FFTs
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3d grid and FFT values/proc = 6776 1800
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3d grid and FFT values/proc = 4312 960
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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@ -107,7 +107,7 @@ SHAKE stats (type/ave/delta) on step 0
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14 0.96 0
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18 0.957206 4.37979e-05
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31 104.519 0.00396029
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Per MPI rank memory allocation (min/avg/max) = 16.81 | 16.82 | 16.83 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
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Step Temp TotEng PotEng KinEng E_pair E_bond f_2
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0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0
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10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504
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@ -118,7 +118,7 @@ Step Temp TotEng PotEng KinEng E_pair E_bond f_2
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60 273.01449 -5217.7381 -6316.1026 1098.3646 -6406.4709 21.800931 0.92327815
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70 274.67549 -5221.0246 -6326.0716 1105.047 -6409.7721 19.41235 0.0016975896
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80 273.74824 -5224.7613 -6326.0778 1101.3165 -6418.5055 19.206793 0.48550348
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90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3467 21.124789 0.5468014
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90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3466 21.124789 0.5468014
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SHAKE stats (type/ave/delta) on step 100
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4 1.111 2.06868e-06
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6 0.996999 2.09521e-06
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@ -128,31 +128,31 @@ SHAKE stats (type/ave/delta) on step 100
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14 0.959999 0
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18 0.9572 9.14098e-06
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31 104.52 0.000760401
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100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372
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100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.009478437
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101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332
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Loop time of 1.23137 on 2 procs for 101 steps with 2004 atoms
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Loop time of 1.16767 on 4 procs for 101 steps with 2004 atoms
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Performance: 14.173 ns/day, 1.693 hours/ns, 82.022 timesteps/s
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99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
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Performance: 14.947 ns/day, 1.606 hours/ns, 86.497 timesteps/s
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97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.97985 | 0.98197 | 0.98409 | 0.2 | 79.75
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Bond | 0.0033333 | 0.0035326 | 0.003732 | 0.3 | 0.29
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Kspace | 0.096567 | 0.098457 | 0.10035 | 0.6 | 8.00
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Neigh | 0.088877 | 0.088888 | 0.088898 | 0.0 | 7.22
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Comm | 0.018255 | 0.018347 | 0.01844 | 0.1 | 1.49
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Output | 0.00024843 | 0.00031161 | 0.00037479 | 0.0 | 0.03
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Modify | 0.037596 | 0.037645 | 0.037695 | 0.0 | 3.06
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Other | | 0.00222 | | | 0.18
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Pair | 0.84633 | 0.86651 | 0.88617 | 1.6 | 74.21
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Bond | 0.0010614 | 0.0027132 | 0.004288 | 3.0 | 0.23
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Kspace | 0.095008 | 0.1162 | 0.13491 | 4.3 | 9.95
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Neigh | 0.07834 | 0.078424 | 0.078516 | 0.0 | 6.72
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Comm | 0.03314 | 0.033299 | 0.033426 | 0.1 | 2.85
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Output | 0.00036979 | 0.00076199 | 0.0019338 | 0.0 | 0.07
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Modify | 0.063471 | 0.064011 | 0.065312 | 0.3 | 5.48
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Other | | 0.005751 | | | 0.49
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Nlocal: 1002 ave 1010 max 994 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8639.5 ave 8651 max 8628 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 353980 ave 355907 max 352054 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nlocal: 501 ave 512 max 492 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Nghost: 6570.25 ave 6604 max 6529 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Neighs: 176990 ave 181122 max 173551 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Total # of neighbors = 707961
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Ave neighs/atom = 353.274
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@ -35,10 +35,16 @@ version = "2.4.3"
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# known checksums for different PLUMED versions. used to validate the download.
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checksums = { \
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'2.4.2' : '0f66f24b4c763ae8b2f39574113e9935', \
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'2.4.3' : 'dc38de0ffd59d13950d8f1ef1ce05574', \
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'2.4.2' : '88188743a6e03ef076e5377d03ebb0e7', \
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'2.4.3' : 'b1be7c48971627febc11c61b70767fc5', \
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'2.5b' : 'e341bdef469be1da058b8a0b97a3db22', \
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}
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#checksums = { \
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# '2.4.2' : '0f66f24b4c763ae8b2f39574113e9935', \
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# '2.4.3' : 'dc38de0ffd59d13950d8f1ef1ce05574', \
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# }
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# print error message or help
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def error(str=None):
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if not str: print(help)
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@ -146,8 +152,10 @@ if (not buildflag and not pathflag):
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# download and unpack plumed2 tarball
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if buildflag:
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url = "https://github.com/plumed/plumed2/archive/v%s.tar.gz" % version
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filename = "v%s.tar.gz" %version
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url = "https://github.com/plumed/plumed2/releases/download/v%s/plumed-src-%s.tgz" % (version,version)
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filename = "plumed-src-%s.tar.gz" %version
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#url = "https://github.com/plumed/plumed2/archive/v%s.tar.gz" % version
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#filename = "v%s.tar.gz" %version
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print("Downloading plumed ...")
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geturl(url,filename)
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@ -156,22 +164,26 @@ if buildflag:
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if not checkmd5sum(checksums[version],filename):
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error("Checksum for plumed2 library does not match")
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print("Unpacking plumed2 tarball ...")
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if os.path.exists("%s/plumed2-%s" % (homepath,version)):
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cmd = 'rm -rf "%s/plumed2-%s"' % (homepath,version)
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print("Unpacking plumed2 source tarball ...")
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if os.path.exists("%s/plumed-%s" % (homepath,version)):
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cmd = 'rm -rf "%s/plumed-%s"' % (homepath,version)
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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#if os.path.exists("%s/plumed2-%s" % (homepath,version)):
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# cmd = 'rm -rf "%s/plumed2-%s"' % (homepath,version)
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# subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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if os.path.exists("%s/plumed2" % (homepath)):
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cmd = 'rm -rf "%s/plumed2"' % (homepath)
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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cmd = 'cd "%s"; tar -xzvf v%s.tar.gz' % (homepath,version)
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cmd = 'cd "%s"; tar -xzvf %s' % (homepath,filename)
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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os.remove("%s/v%s.tar.gz" % (homepath,version))
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os.remove("%s/%s" % (homepath,filename))
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# build plumed
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if buildflag:
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print("Building plumed ...")
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cmd = 'cd %s/plumed2-%s; ./configure --prefix=%s/plumed2 ; make ; make install' % (homepath,version,homepath)
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cmd = 'cd %s/plumed-%s; ./configure --prefix=%s/plumed2 --enable-static-patch ; make ; make install' % (homepath,version,homepath)
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#cmd = 'cd %s/plumed2-%s; ./configure --prefix=%s/plumed2 --enable-static-patch ; make ; make install' % (homepath,version,homepath)
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txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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print(txt.decode('UTF-8'))
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#
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@ -190,4 +202,5 @@ if linkflag:
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if os.path.isfile("Makefile.lammps.static"):
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print("Creating Makefile.lammps")
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cmd = 'cat liblink/plumed/src/lib/Plumed.inc.static Makefile.lammps.static > Makefile.lammps'
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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@ -34,25 +34,9 @@
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#include "pair.h"
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/*
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Do not link plumed directly but rather do it at runtime
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Use statically linked C++ interface to plumed
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*/
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#define __PLUMED_WRAPPER_LINK_RUNTIME 1
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/*
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Make sure the inline C++ interface is not included here.
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Should not be necessary, but it doesn't hurt.
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*/
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#define __PLUMED_WRAPPER_CXX 0
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/*
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Tell Plumed.h to emit the whole implementation
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*/
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#define __PLUMED_WRAPPER_IMPLEMENTATION 1
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/*
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Emit fortran wrappers
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*/
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#define __PLUMED_WRAPPER_FORTRAN 1
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#define __PLUMED_WRAPPER_CXX 1
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#include "plumed/wrapper/Plumed.h"
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